Bioinformatics support for the Baker Institute: team and projects update
Domain Bioinformatics
Sergio Ruiz Carmona, Artika Nath and Rodrigo Canovas September 2021
Provide Support Role for all Baker Laboratories
Started
2017
2021
❖3 Bioinformaticians
❖35 projects – completed
●Data analysis
●5 grant applications
●4 manuscripts published
❖17 projects – ongoing
●5 manuscripts in preparation
●1 manuscript submitted
Major underpinning ANALYTICS infrastructure for Baker
MISSION: To build bioinformatics capacity at the Baker Institute through collaboration, support and training
CAPABILITES: Analysis of data and
•Genomics
•Epigenomics
•Transcriptomics (Bulk & single cell)
•Proteomics
•Metabolomics
•Metagenomics
•Blood cell traits
APPROACHES:
•Statistical analysis
•Machine learning
•Network analysis
•High dimensional data normalisation, processing & visualisation
•Design of computational algorithms
Who we are
Artika Nath
●PhD in Bioinformatics (University Of Melbourne)
○Integrative genomics
○Functional analysis
○Network/Cluster analysis
○Data & Statistical Analysis
○Gene expression analysis (Bulk & Single Cell)
○GWAS (Univariate & Multivariate)
○eQTL and Colocalisation Analysis
●Postdoctoral Researcher / Bioinformatician (Baker)
○Since 2018
○Integrative genomics
○Data science, manipulation, visualisation
○Analysis of transcriptomics, metabolomics, protein data
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●Cambridge Baker Systems Genomics Initiative
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○5000 samples with
○eQTL analysis, colocalisation analysis, coexpression network analysis, Integration with other molecular traits
Nath et al., 2019
Nath et al., 2017
Nath et al., 2019
Nath et al., 2019
Investigate the transcriptomic profile of reduced cardiac
Excessive
The global transcriptomic profile of |
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Prof. Rebecca Ritchie’s Lab |
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Diabetic
Diabetic - OGA
OGA - reduces
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Enrichment analysis revealed that |
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OGA administration altered pathway |
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associated with cardiac remodelling. |
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Prakoso, Nath, et al - Manuscript in Prep.
Rodrigo Cánovas
●PhD - Engineering, The University of Melbourne, Australia
○In the disciplines of Bioinformatics Software and Coding and Information Theory
○Finished in 2015
○Practical Compression for
●Postdoctoral Researcher, LIRMM and IBC, France
○From 2015 to end of 2017
○ Developing algorithms for analysing
●Research Officer / Bioinformatician, Baker Institute, Australia
○Since 2018, Systems Genomics lab
○Genomic risk prediction
○Data science, manipulation and visualization
●Bioinformatics and Computer Science including, between others:
○Genomic risk prediction, survival analysis, design and analysis of algorithms and data structures, indexing, compression, pattern matching , machine learning, deep learning, data analysis
(Status: manuscript of exploratory analysis )
Among UK Biobank participants who were
I.Does the predictors of genetic predisposition for VTE helps to predict the development of
II. Considering only individuals that tested positive. Are predictors of genetic predisposition for VTE associated with an increase in the mortality rate from
III. Association of
Parameters Correlation plot
Predicting
RDH11 target role in humans
Collaboration with Baker’s Lipid Metabolism and
Dr Michael Keating
Among the UK Biobank:
I.Understand what role that RDH11 might be playing in humans
II.Check if RDH11 is associated with phenotypes linked to these pathways A. (eg. phenotypes associated with variation at the RDH11 locus)
Sergio Ruiz Carmona
●PhD in Computational Biology and Drug Discovery
○Finished in 2017 in Barcelona (Spain)
○Method development and applications in drug design
●Postdoc in drug discovery for blood disorders
○In Barcelona (Spain)
○Drug patent &
○EMBO
●Research Officer / Bioinformatician @Baker Institute
○Since early 2019, Systems Genomics lab
○Protein structure genomics
○Data science, manipulation and visualization
○Bioinformatics and gene expression analysis
○Machine learning and High Performance Computing
○UK Biobank
○Web development and interactive applications / dashboards
Oxygen Pathway analysis in CTEPH patients
Collaboration with the
Dr. Erin Howden
Dr. Guido Claessen
A/Prof Andre La Gerche
Interactive
Shiny App
Baker quarterly publication award (presentation next Tuesday, 7th)
lncRNAs in physiological and pathological hypertrophy
Collaboration with the
Dr. Jenny Ooi
Prof. Julie McMullen
TrainingPeaks - Athlete data analysis
~200 athletes
60.000 training activities
Collaboration with the
Kristel Janssens
Dr. Guido Claessen
A/Prof Andre La Gerche
How does it work?
○How can Baker researchers engage with us?
○How does the process look like?
○What can you expect from us?
How much is it?
We work with a collaborative model
-Authorship in papers
-Grant participation
-General advice
Project requests
https://intranet.baker.edu.au/resear
technologies/bioinformatics-
Search
“Domain Bioinformatics”
on the intranet search box
Research resources >
Platform Technologies >
Bioinformatics Program >
Domain Bioinformatics
Request & project timeline
First email |
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analysis & |
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(Full team) |
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analysis & |
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Ideal situation
Background |
Ideal |
information |
Outcome |
Data
analysis
Also...
UK Biobank Projects
Recruited Individuals
Recruited ~500,000 UK individuals (not families) between 2006 – 2010
Image obtained from the UKB webpage
UK Biobank Timeline
DataNightingale Health’s study
Blood samples
120,000
20202021
Exome
sequencing of
200,000
Image adapted from R. Collins UKB slides
Principles of accessing UK Biobank
●Open access resource, available for bona fide researchers to conduct
●Researchers are obliged to return their results to UK Biobank so they can be shared with others
●Any work/presentation/publication must include the following phrase:
“This research has been conducted using the UK Biobank Resource under application number 55469”
Using the
●Access the UK Biobank
○Register with the UK Biobank
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○Contact Mike Inouye or Domain Bioinformatician Team to:
■Be added to Baker’s approved UKB project
●Rules of how to use the UKB data:
○If you have data science training specific arrangements can be made to grant access to the data
○All UKB data must be and remain on the server (common Baker cluster)
○NO UKB DATA IS TO BE TRANSFERRED OFF THE SERVER
Using the
●Suggested Project Pipeline:
○Request access to the UKB
○Explore what have been done already
○Submit a project request to the Domain Bioinformatics group
○Before the first meeting check on the UKB showcase which data would be useful
■Some links that may help:
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General UKB web page
Operative procedure codes https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=41272
○Create some amazing research
○Report results back to the UK Biobank
Thank you!
Domain Bioinformatics
Sergio Ruiz Carmona, Artika Nath and Rodrigo Canovas September 2021